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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DNA POLYMERASE III BETA SUBUNIT (EUBREC_0002; ERE_29750) FROM EUBACTERIUM RECTALE ATCC 33656 AT 2.26 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Jul 11  (Deposition) - 10 Aug 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Clamp, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Dna Polymerase Iii Beta Subunit (Eubrec_0002; Ere_29750) From Eubacterium Rectale Atcc 33656 At 2. 26 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE III, BETA SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EUBREC_0002
    Organism Scientific: EUBACTERIUM RECTALE
    Organism Taxid: 515619
    Strain: ATCC 33656 / VPI 0990

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 51)

Asymmetric/Biological Unit (5, 51)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3EDO18Ligand/Ion1,2-ETHANEDIOL
4MSE24Mod. Amino AcidSELENOMETHIONINE
5PGR2Ligand/IonR-1,2-PROPANEDIOL

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:249 , SER A:250 , TYR A:252 , LYS A:350 , HOH A:644BINDING SITE FOR RESIDUE PGR A 373
02AC2SOFTWARETHR A:133 , VAL A:137 , GLN A:140BINDING SITE FOR RESIDUE ACT A 376
03AC3SOFTWAREASP A:307BINDING SITE FOR RESIDUE ACT A 378
04AC4SOFTWAREASN A:47 , MSE A:49 , GLU A:50 , GLY A:52 , VAL A:233 , ARG A:235BINDING SITE FOR RESIDUE EDO A 382
05AC5SOFTWARELYS A:19 , ALA A:20 , VAL A:21 , PRO A:22 , ASP A:48 , LYS A:197 , EDO A:388BINDING SITE FOR RESIDUE EDO A 383
06AC6SOFTWAREGLU A:54 , ASN A:229 , THR A:231BINDING SITE FOR RESIDUE EDO A 384
07AC7SOFTWAREPRO A:119 , TYR A:120 , VAL A:121 , ARG A:123BINDING SITE FOR RESIDUE EDO A 385
08AC8SOFTWAREGLU A:160 , ARG A:167BINDING SITE FOR RESIDUE EDO A 386
09AC9SOFTWARETHR A:23 , GLU A:201 , LYS A:204 , EDO A:383 , HOH A:400 , HOH A:460BINDING SITE FOR RESIDUE EDO A 388
10BC1SOFTWAREASP A:251 , TYR A:252BINDING SITE FOR RESIDUE EDO A 389
11BC2SOFTWAREASN A:285 , ILE A:315 , MSE A:316BINDING SITE FOR RESIDUE EDO A 391
12BC3SOFTWAREGLU A:226 , GLU A:228 , ASP B:213BINDING SITE FOR RESIDUE EDO A 392
13BC4SOFTWAREPHE A:132 , GLU A:136 , ARG A:139 , ASP A:332BINDING SITE FOR RESIDUE EDO A 394
14BC5SOFTWARELYS A:243 , GLN A:246BINDING SITE FOR RESIDUE EDO A 397
15BC6SOFTWAREASP B:251 , TYR B:252 , ASP B:253 , HOH B:642BINDING SITE FOR RESIDUE PGR B 374
16BC7SOFTWAREASN B:47 , MSE B:49 , GLU B:50 , LEU B:51 , GLY B:52 , PRO B:119 , HIS B:222 , VAL B:233BINDING SITE FOR RESIDUE ACT B 375
17BC8SOFTWARELYS B:19 , VAL B:21 , PRO B:22 , ASP B:48 , LYS B:197 , GLU B:201BINDING SITE FOR RESIDUE ACT B 377
18BC9SOFTWAREGLU B:262BINDING SITE FOR RESIDUE ACT B 379
19CC1SOFTWARETYR B:339 , LYS B:350BINDING SITE FOR RESIDUE EDO B 380
20CC2SOFTWAREILE B:4 , CYS B:5 , SER B:6BINDING SITE FOR RESIDUE EDO B 381
21CC3SOFTWAREGLU B:54 , ASN B:229 , THR B:231 , HOH B:603BINDING SITE FOR RESIDUE EDO B 387
22CC4SOFTWAREGLU B:160 , GLU B:162 , ARG B:167BINDING SITE FOR RESIDUE EDO B 390
23CC5SOFTWARELYS B:104 , HOH B:430 , HOH B:471BINDING SITE FOR RESIDUE EDO B 393
24CC6SOFTWAREGLN B:200 , LYS B:204 , HOH B:410BINDING SITE FOR RESIDUE EDO B 395
25CC7SOFTWAREARG B:139 , HOH B:536BINDING SITE FOR RESIDUE EDO B 396
26CC8SOFTWAREARG B:123BINDING SITE FOR RESIDUE CL B 398

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T0P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T0P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T0P)

(-) Exons   (0, 0)

(no "Exon" information available for 3T0P)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:365
 aligned with C4Z938_AGARV | C4Z938 from UniProtKB/TrEMBL  Length:370

    Alignment length:366
                             1                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359      
         C4Z938_AGARV     - -MKLICSKANLLKGVNIVSKAVPTRTTMAILECILIDASANEIKLMANDMELGIETIIDGTIEERGIIALDAKIFSEIVRKLPDNDVTIETDASFKTVISCEKAKFNIIGKSGDDFSYIPYVERNESIVLSQFTLKEVIRQTIFSIADNDNNKLMTGELFEIEENKLRVVSLDGHRISIRYIEMKNHYDSKKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSRLIEGEYFKIDQMLSSDYDTKVRINKRELLDCIDRATLLVKEGDKKPIIMNITDGNMELRINSFIGSMNEDIDIDKDGKDIMIGFNPKFFIDALRVIDEEEVNLYMVNPKAPCFIKDDEGKFIYLILPVNF 365
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhh.....hhhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhhh...eeeeee....eeeeee..eeeeee..hhhhh..........eeeeehhhhhhhhhhhhhhh......hhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhhh......eeeeeee..eeeeee..eeeeee........hhhhh.....eeeeeehhhhhhhhhhhhh....-....eeeeee..eeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhh.....eeeeee......eeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3t0p A   0 GmKLICSKANLLKGVNIVSKAVPTRTTmAILECILIDASANEIKLmANDmELGIETIIDGTIEERGIIALDAKIFSEIVRKLPDNDVTIETDASFKTVISCEKAKFNIIGKSGDDFSYIPYVERNESIVLSQFTLKEVIRQTIFSIADNDNNKLmTGELFEIEENKLRVVSLDGHRISIRYIEmKNHYDSKKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSRLIEGEYFKIDQmLSSDYDTKVRINKRELLDCIDRATLLVKE-DKKPIImNITDGNmELRINSFIGSmNEDIDIDKDGKDImIGFNPKFFIDALRVIDEEEVNLYmVNPKAPCFIKDDEGKFIYLILPVNF 365
                             |       9        19       |29        39     |  49        59        69        79        89        99       109       119       129       139       149    |  159       169       179   |   189       199       209       219       229       239       249       259       269      |279    |  289 |     299  |    309      |319       329       339|      349       359      
                             |                        27-MSE            45-MSE                                                                                                      154-MSE                      183-MSE                                                         247-MSE                      276 |     |      |        302-MSE       316-MSE                 340-MSE                     
                             1-MSE                                          49-MSE                                                                                                                                                                                                                              278     |      |                                                                          
                                                                                                                                                                                                                                                                                                                      284-MSE  |                                                                          
                                                                                                                                                                                                                                                                                                                             291-MSE                                                                      


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with C4Z938_AGARV | C4Z938 from UniProtKB/TrEMBL  Length:370

    Alignment length:368
                             1                                                                                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359        
         C4Z938_AGARV     - -MKLICSKANLLKGVNIVSKAVPTRTTMAILECILIDASANEIKLMANDMELGIETIIDGTIEERGIIALDAKIFSEIVRKLPDNDVTIETDASFKTVISCEKAKFNIIGKSGDDFSYIPYVERNESIVLSQFTLKEVIRQTIFSIADNDNNKLMTGELFEIEENKLRVVSLDGHRISIRYIEMKNHYDSKKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSRLIEGEYFKIDQMLSSDYDTKVRINKRELLDCIDRATLLVKEGDKKPIIMNITDGNMELRINSFIGSMNEDIDIDKDGKDIMIGFNPKFFIDALRVIDEEEVNLYMVNPKAPCFIKDDEGKFIYLILPVNFNT 367
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhh......hhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhhh...eeeeee....eeeeee..eeeeee..hhhhh..........eeeeehhhhhhhhhhhhhhh......hhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhhh......eeeeeee..eeeeee..eeeeee........hhhhh.....eeeeeehhhhhhhhhhhhh.........eeeeee..eeeeeee....eeeeeee.eeee..eeeeehhhhhhhhhh.....eeeeee......eeee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0p B   0 GmKLICSKANLLKGVNIVSKAVPTRTTmAILECILIDASANEIKLmANDmELGIETIIDGTIEERGIIALDAKIFSEIVRKLPDNDVTIETDASFKTVISCEKAKFNIIGKSGDDFSYIPYVERNESIVLSQFTLKEVIRQTIFSIADNDNNKLmTGELFEIEENKLRVVSLDGHRISIRYIEmKNHYDSKKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSRLIEGEYFKIDQmLSSDYDTKVRINKRELLDCIDRATLLVKEGDKKPIImNITDGNmELRINSFIGSmNEDIDIDKDGKDImIGFNPKFFIDALRVIDEEEVNLYmVNPKAPCFIKDDEGKFIYLILPVNFNT 367
                             |       9        19       |29        39     |  49        59        69        79        89        99       109       119       129       139       149    |  159       169       179   |   189       199       209       219       229       239       249       259       269       279    |  289 |     299  |    309      |319       329       339|      349       359        
                             1-MSE                    27-MSE            45-MSE                                                                                                      154-MSE                      183-MSE                                                         247-MSE                              284-MSE  |        302-MSE       316-MSE                 340-MSE                       
                                                                            49-MSE                                                                                                                                                                                                                                           291-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3T0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T0P)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (C4Z938_AGARV | C4Z938)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0009360    DNA polymerase III complex    The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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